In contrast with the earliest models suggesting that it functioned only as messenger, RNA is now known to participate in a myriad of essential biological processes, ranging from gene expression through protein manufacturing. Short double-stranded RNAs participate in selective degradation of messenger RNA transcripts (RNA interference);folded RNAs can catalyze reactions, or switch genes on and off;in conjunction with numerous proteins, RNAs fold into large molecular machines, like the protein-manufacturing ribosome. Furthermore, because small RNAs can be designed to selectivity bind specific targets, these molecules have enormous potential as therapeutics. These widely varying roles are enabled by RNA's structural versatility. We propose to test new hypotheses about the roles of ions and RNA architecture in RNA self-assembly or folding. We will use time resolved small angle x-ray scattering to report the time-dependent formation of global structures, time-resolved hydroxyl radical footprinting to report the formation of individual contacts within the folding molecule, and time-resolved fluorescence methods to report specific intramolecular distances during folding. To enhance experimental studies, we propose to develop efficient atomically detailed simulations of the kinetics and thermodynamics of RNA folding. Initially, these coupled tools will be applied to further quantify the important role of ions in RNA folding. We will also study folding of different classes of RNA enzymes or ribozymes to explore the role of RNA architecture in folding. Our long term goal is to understand the factors involved in RNA folding. Such knowledge is essential for the efficient development and application of RNA-based therapeutics.

Public Health Relevance

RNA molecules can """"""""fold"""""""" into biologically active structures that carry out a wide variety of functions. The numerous roles assumed by RNA highlight its usefulness and its great potential as a therapeutic molecule or a target for other therapeutics. These studies will enable us to better understand how RNA structures assemble, thus will teach us how to more efficiently design RNAs for application in medicine or biotechnology.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM085062-03
Application #
8134861
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2009-09-01
Project End
2013-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
3
Fiscal Year
2011
Total Cost
$323,959
Indirect Cost
Name
Cornell University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
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Chen, Yujie; Tokuda, Joshua M; Topping, Traci et al. (2017) Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 114:334-339
Plumridge, Alex; Meisburger, Steve P; Andresen, Kurt et al. (2017) The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45:3932-3943
Tokuda, Joshua M; Pabit, Suzette A; Pollack, Lois (2016) Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev 8:139-149
Nguyen, Hung T; Pabit, Suzette A; Pollack, Lois et al. (2016) Extracting water and ion distributions from solution x-ray scattering experiments. J Chem Phys 144:214105
Chen, Yujie; Pollack, Lois (2016) SAXS studies of RNA: structures, dynamics, and interactions with partners. Wiley Interdiscip Rev RNA 7:512-26
Sutton, Julie L; Pollack, Lois (2015) Tuning RNA Flexibility with Helix Length and Junction Sequence. Biophys J 109:2644-53
Meisburger, Steve P; Pabit, Suzette A; Pollack, Lois (2015) Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophys J 108:2886-95
Nguyen, Hung T; Pabit, Suzette A; Meisburger, Steve P et al. (2014) Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. J Chem Phys 141:22D508
Chen, Yujie; Tokuda, Joshua M; Topping, Traci et al. (2014) Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Res 42:8767-76

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